Probes (NEO and TAP) were amplified (oligonucleotides listed in Additional file 8 – Table S5) and radioactively labeled with α-[P32]-dCTP (10 μCi/μl; 3,000 Ci/mmol) (Amersham Biosciences) using the Nick Translation System (Invitrogen), according to the manufacturer’s instructions. Real-time RT-PCR Total RNA was extracted from 1 × 108 cells by RNeasy Kit (Qiagen, Hilden, Germany) according to manufacturer’s
instructions. Single strand cDNA was obtained as follows: 1 μg of RNA and 1 μM oligo dT were mixed and incubated for 10 min at 70°C. Then, 4 μl of Improm-II buffer (Promega, Madison, USA), 3 mM MgCl2, 0.5 mM each dNTP, 40 U RNaseOUT (Invitrogen) and 2 μl Improm-II Reverse Transcriptase (Promega)
GSK1838705A were mixed in a final volume of 20 μl and incubated for 2 h at 42°C. The product was then purified with Microcon(r) YM-30 (Millipore, Massachusetts, USA) and resuspended with water at the concentration of 2 ng μl-1. PCR reactions included 10 ng or 0.4-50 ng (standard curve) of single strand cDNA samples as template, 0.25 μmol of each oligonucleotide, H2B histone oligonucleotides for normalization (listed in Additional file 8 – Table S5) and SYBR(r) Green CCI-779 PCR Master Mix (Applied Biosystems, Foster City, USA). A sample from T. cruzi wild type was used as a negative control. The reactions were Selleck GNS-1480 performed and the standard curve was determined in triplicate and all PCR runs were carried out in an Applied Biosystems 7500 Real-Time PCR System. Data was acquired with the Real-Time PCR System Detection Software v1.4 (Applied Biosystems). Analysis was performed using an average of three quantifications for each sample. Western blot analysis For immunoblotting analysis, cell lysates (from 5 Farnesyltransferase × 106 parasites or, for TAP procedures, 5 to 15 μg of total protein and
25-50% of the digestion) were separated by SDS-PAGE using 13% polyacrylamide gels. Protein bands were transferred onto a nitrocellulose membrane (Hybond C, Amersham Biosciences) according to standard protocols . Nonspecific binding sites were blocked by incubating the membrane for 1 h in 5% nonfat milk powder and 0.1% Tween-20 in TBS, pH 8.0. The membrane was then incubated for 1 h with either the monoclonal antibody anti-GFP (3.3 μg ml-1) (Molecular Probes(r) – Invitrogen), monoclonal anti-histidine (1.4 – 2.8 μg ml-1) (Amersham Biosciences), monoclonal anti-c-myc clone 9E10 (10 μg ml-1) (Clontech) or polyclonal serum anti-CBP (1:1,000) (Upstate(r)-Millipore) antibodies. For TAP procedures, polyclonal serum anti-L26 ribosomal protein  (1:250) and anti-α2 20S proteasome subunit (1:600) were used. The membrane was washed three times in TBS and was then incubated for 45 min with the secondary antibodies diluted in blocking solution.